Generating standardized image data for testing and calibrating quantification of volumes, surfaces, lengths, and object counts in fibrous and porous materials using X‐ray microtomography

Abstract

Quantification of the structure and composition of biomaterials using micro-CT requires image segmentation due to the low contrast and overlapping radioopacity of biological materials. The amount of bias introduced by segmentation procedures is generally unknown. We aim to develop software that generates three-dimensional models of fibrous and porous structures with known volumes, surfaces, lengths, and object counts in fibrous materials and to provide a software tool that calibrates quantitative micro-CT assessments. Virtual image stacks were generated using the newly developed software TeIGen, enabling the simulation of micro-CT scans of unconnected tubes, connected tubes, and porosities. A realistic noise generator was incorporated. Forty image stacks were evaluated using micro-CT, and the error between the true known and estimated data was quantified. Starting with geometric primitives, the error of the numerical estimation of surfaces and volumes was eliminated, thereby enabling the quantification of volumes and surfaces of colliding objects. Analysis of the sensitivity of the thresholding upon parameters of generated testing image sets revealed the effects of decreasing resolution and increasing noise on the accuracy of the micro-CT quantification. The size of the error increased with decreasing resolution when the voxel size exceeded 1/10 of the typical object size, which simulated the effect of the smallest details that could still be reliably quantified. Open-source software for calibrating quantitative micro-CT assessments by producing and saving virtually generated image data sets with known morphometric data was made freely available to researchers involved in morphometry of three-dimensional fibrillar and porous structures in micro-CT scans.

Vancomycin-releasing cross-linked collagen sponges as wound dressings

“…Three volumes of interest [VOI] (3 mm × 3 mm × sample thickness) were analyzed in each sample. Image-processing and analyses were performed by CTAn (Bruker micro-CT, Kontich, Belgium) and optimized using Test Image Generator software [22]. The porosity (Po) was calculated as: Po = (volume of open + closed pores)/ VOI volume.…”

Mechanical Enhancement of Cytocompatible 3D Scaffolds, Consisting of Hydroxyapatite Nanocrystals and Natural Biomolecules, Through Physical Cross-Linking

“…Specifically, the bands noted at 556 and 596 cm −1 correspond to the v 4 bending modes of O-P-O bond [ 39 , 40 ]. The band at 1016 cm −1 arises from the anti-symmetric v 3 stretching modes of P-O bonds, while the band at 963 cm −1 can be assigned to the symmetric v 1 stretching mode of the phosphate groups (ΡO 4 ) [ 38 , 40 ]. Furthermore, the symmetric stretching mode of OH − ions is attributed to the 3644 cm −1 band, along with the 645 cm −1 band representing the librational mode of hydroxyl groups [ 41 , 42 , 43 , 44 , 45 ].…”

“…Closed pores are registered as any group of black pixels surrounded by white pixels, while open pores are defined as any space located within a solid object or between solid objects, which has any connection in 3D to the space outside the object or objects. Total porosity is the volume of all open plus closed pores as a percent of the total VOI volume CTAn software manual [ 38 ].…”

“…Closed pores are registered as any group of black pixels surrounded by white pixels, while open pores are defined as any space located within a solid object or between solid objects, which has any connection in 3D to the space outside the object or objects. Total porosity is the volume of all open plus closed pores as a percent of the total VOI volume CTAn software manual [38]. Application of a threshold window from: 0.01880 to 0.09044 AT for scaffolds without crosslinking (a) before threshold application and (b) after thresholding; and 0.02022 to 0.09044 AT for scaffolds crosslinked with 0.01% riboflavin (c) before threshold application and (d) after thresholding.…”

Note on the use of different approaches to determine the pore sizes of tissue engineering scaffolds: what do we measure?

“…Prior to structure analysis, the datasets were binarized using an adaptive threshold and despeckle operations in 3D were applied to reduce image noise. These steps were optimized using TeiGen software [ 23 ]. The volume of interest (VOI) subjected to analysis was defined by the shrink-wrap procedure in 3D.…”